In our project I added some custom fields that we want to have in our service desk customer portal but, have those fields not show up when creating regular issues not through SD. Is there a way to do that ?
You should be able to add custom fields and control what screens they are visible in by associating the custom fields to specific screens. One way to do so is to go to the Custom Fields page. To associate fields with specific screens, pull down the gear menu for the field and select Screens.
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